Personally, I'd probably fork out $35 for Dosadi's (the writers of the EZTWAIN library around which Win32::Scanner::EZTWAIN is wrapped) Aquire command line utility. It has a switch which will try to negotiate with your TWAIN device to prevent the user interface being displayed. This is the source of the popups you see when using EZTWAIN rather than EZTWAIN itself.

You can even download a copy and try for 7 days to make sure it does what you need before you purchase.